rs1516971

Variant names:

• chr8-128529854-T-C
• rs1516971
• ENST00000520766.5:n.57+31216A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000520766.5(LINC00824):​n.57+31216A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,082 control chromosomes in the GnomAD database, including 3,409 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.18 (3409 hom., cov: 32)
• Consequence: LINC00824 ENST00000520766.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72
• Publications: 34 publications found

Genes affected

LINC00824 (HGNC:50281): (long intergenic non-protein coding RNA 824)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00824	NR_121672.1	n.508+31216A>G		intron_variant	Intron 2 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00824	ENST00000520766.5	n.57+31216A>G		intron_variant	Intron 1 of 5	5
LINC00824	ENST00000756796.1	n.425-12951A>G		intron_variant	Intron 2 of 2
LINC00824	ENST00000756797.1	n.426-12951A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27787 AN: 151966 Hom.: 3405 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.0303

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.163

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.183 AC: 27816 AN: 152082 Hom.: 3409 Cov.: 32 AF XY: 0.180 AC XY: 13354 AN XY: 74348

African (AFR) AF: 0.346 AC: 14330 AN: 41440

American (AMR) AF: 0.106 AC: 1626 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 378 AN: 3468

East Asian (EAS) AF: 0.0298 AC: 154 AN: 5172

South Asian (SAS) AF: 0.117 AC: 563 AN: 4824

European-Finnish (FIN) AF: 0.126 AC: 1328 AN: 10576

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 8947 AN: 67998

Other (OTH) AF: 0.164 AC: 347 AN: 2114

Alfa AF: 0.151 Hom.: 4663

Bravo AF: 0.189

Asia WGS AF: 0.0970 AC: 337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.13
DANN	Benign	0.23
PhyloP100		-1.7

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1516971; hg19: chr8-129542100;